mirror of
https://github.com/johrpan/geposanui.git
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105 lines
2.4 KiB
R
105 lines
2.4 KiB
R
#' Create a GSEA page.
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#' @noRd
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gsea_ui <- function(id) {
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verticalLayout(
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filters_ui(NS(id, "filters")),
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div(
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class = "flow-layout",
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actionButton(
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NS(id, "gsea_run"),
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"Update analysis",
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class = "btn-primary"
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),
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a(
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"Powered by g:Profiler",
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href = "https://biit.cs.ut.ee/gprofiler/gost",
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target = "_blank",
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style = "margin-left: 16px"
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)
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),
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div(
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style = "margin-top: 16px",
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plotly::plotlyOutput(NS(id, "plot")),
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),
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div(
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style = "margin-top: 16px",
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DT::DTOutput(NS(id, "details"))
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)
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)
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}
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#' Create a server for the comparison editor.
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#'
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#' @param id ID for namespacing the inputs and outputs.
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#' @param ranking The ranking to be analyzed.
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#'
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#' @noRd
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gsea_server <- function(id, ranking) {
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moduleServer(id, function(input, output, session) {
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ranking_filtered <- filters_server("filters", ranking)
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gsea_analysis <- reactive({
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withProgress(
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message = "Querying g:Profiler",
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value = 0.0,
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{ # nolint
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setProgress(0.2)
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gprofiler2::gost(
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ranking_filtered()$gene,
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custom_bg = ranking()$gene,
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domain_scope = "custom_annotated"
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)
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}
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)
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}) |>
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bindCache(ranking_filtered()) |>
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bindEvent(input$gsea_run, ignoreNULL = FALSE)
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output$plot <- plotly::renderPlotly({
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gprofiler2::gostplot(
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gsea_analysis(),
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capped = FALSE,
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interactive = TRUE
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)
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})
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output$details <- DT::renderDT({
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data <- data.table(gsea_analysis()$result)
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setorder(data, p_value)
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data[, total_ratio := term_size / effective_domain_size]
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data[, query_ratio := intersection_size / query_size]
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data[, increase := (query_ratio - total_ratio) / total_ratio]
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data <- data[, .(
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source,
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term_name,
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total_ratio,
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query_ratio,
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increase,
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p_value
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)]
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DT::datatable(
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data,
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rownames = FALSE,
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colnames = c(
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"Source",
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"Term",
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"Total ratio",
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"Query ratio",
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"Increase",
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"p-value"
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),
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options = list(
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pageLength = 25
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)
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) |>
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DT::formatRound("p_value", digits = 4) |>
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DT::formatPercentage(
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c("total_ratio", "query_ratio", "increase"),
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digits = 2
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)
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})
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})
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}
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